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Yorodumi- EMDB-1828: Structural basis for scaffolding-mediated assembly and maturation... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1828 | |||||||||
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Title | Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus | |||||||||
Map data | This is the in situ portal segmented out from the P22 procapsid 8.7-Angstrom asymmetric reconstruction, and 12-fold symmetrized. | |||||||||
Sample |
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Keywords | bacteriophage / phage / P22 / procapsid / scaffolding / portal / asymmetric reconstruction / assembly / dsDNA virus | |||||||||
Biological species | Enterobacteria phage P22 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.7 Å | |||||||||
Authors | Chen D-H / Baker ML / Hryc CF / DiMaio F / Jakana J / Wu W / Dougherty M / Haase-Pettingell C / Schmid MF / Jiang W ...Chen D-H / Baker ML / Hryc CF / DiMaio F / Jakana J / Wu W / Dougherty M / Haase-Pettingell C / Schmid MF / Jiang W / Baker D / King JA / Chiu W | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2011 Title: Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Authors: Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / ...Authors: Dong-Hua Chen / Matthew L Baker / Corey F Hryc / Frank DiMaio / Joanita Jakana / Weimin Wu / Matthew Dougherty / Cameron Haase-Pettingell / Michael F Schmid / Wen Jiang / David Baker / Jonathan A King / Wah Chiu / Abstract: Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This ...Formation of many dsDNA viruses begins with the assembly of a procapsid, containing scaffolding proteins and a multisubunit portal but lacking DNA, which matures into an infectious virion. This process, conserved among dsDNA viruses such as herpes viruses and bacteriophages, is key to forming infectious virions. Bacteriophage P22 has served as a model system for this study in the past several decades. However, how capsid assembly is initiated, where and how scaffolding proteins bind to coat proteins in the procapsid, and the conformational changes upon capsid maturation still remain elusive. Here, we report Cα backbone models for the P22 procapsid and infectious virion derived from electron cryomicroscopy density maps determined at 3.8- and 4.0-Å resolution, respectively, and the first procapsid structure at subnanometer resolution without imposing symmetry. The procapsid structures show the scaffolding protein interacting electrostatically with the N terminus (N arm) of the coat protein through its C-terminal helix-loop-helix motif, as well as unexpected interactions between 10 scaffolding proteins and the 12-fold portal located at a unique vertex. These suggest a critical role for the scaffolding proteins both in initiating the capsid assembly at the portal vertex and propagating its growth on a T = 7 icosahedral lattice. Comparison of the procapsid and the virion backbone models reveals coordinated and complex conformational changes. These structural observations allow us to propose a more detailed molecular mechanism for the scaffolding-mediated capsid assembly initiation including portal incorporation, release of scaffolding proteins upon DNA packaging, and maturation into infectious virions. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1828.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-1828-v30.xml emd-1828.xml | 11.2 KB 11.2 KB | Display Display | EMDB header |
Images | EMD-1828.png | 187.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1828 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1828 | HTTPS FTP |
-Validation report
Summary document | emd_1828_validation.pdf.gz | 193.6 KB | Display | EMDB validaton report |
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Full document | emd_1828_full_validation.pdf.gz | 192.7 KB | Display | |
Data in XML | emd_1828_validation.xml.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1828 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1828 | HTTPS FTP |
-Related structure data
Related structure data | 1824C 1825C 1826C 1827C 2xyyC 2xyzC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1828.map.gz / Format: CCP4 / Size: 300.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the in situ portal segmented out from the P22 procapsid 8.7-Angstrom asymmetric reconstruction, and 12-fold symmetrized. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : in situ portal inside bacteriophage P22 wild-type procapsid
Entire | Name: in situ portal inside bacteriophage P22 wild-type procapsid |
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Components |
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-Supramolecule #1000: in situ portal inside bacteriophage P22 wild-type procapsid
Supramolecule | Name: in situ portal inside bacteriophage P22 wild-type procapsid type: sample / ID: 1000 / Details: The in situ portal sits inside the capsid shell / Oligomeric state: Dodecamer / Number unique components: 1 |
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Molecular weight | Experimental: 1 MDa / Theoretical: 1 MDa |
-Macromolecule #1: P22 procapsid in situ portal
Macromolecule | Name: P22 procapsid in situ portal / type: protein_or_peptide / ID: 1 / Name.synonym: P22 procapsid in situ portal Details: The in situ portal sits at one of the 12 vertices of P22 procapsid Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes |
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Source (natural) | Organism: Enterobacteria phage P22 (virus) |
Molecular weight | Experimental: 1 MDa / Theoretical: 1 MDa |
Recombinant expression | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.6 / Details: 50 mM Tris pH 7.6, 25 mM NaCl, 2mM EDTA |
Grid | Details: 400 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 101 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 101 K / Max: 101 K / Average: 101 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Specialist optics | Energy filter - Name: Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Jun 2, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 10000 (10k x 10k) / Digitization - Sampling interval: 9 µm / Number real images: 1120 / Average electron dose: 20 e/Å2 Details: Some particles imaged on SO163 film were merged with the CCD data. The pixel size was scaled to be 2.12 Angstrom per pixel Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 40000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000 |
Sample stage | Specimen holder: Side entry / Specimen holder model: JEOL |
-Image processing
Details | The particles were selected using an automatic selection program. |
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CTF correction | Details: Each CCD frame |
Final reconstruction | Applied symmetry - Point group: C12 (12 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: OTHER Software - Name: Multi-Path Simulated Annealing Optimization algorithm Details: The in situ portal was segmented from the asymmetric reconstruction of P22 procapsid and then 12-fold symmetrized Number images used: 43850 |
Final angle assignment | Details: EMAN:az, alt, phi |